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‎.github/workflows/check-bioc.yml‎

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@@ -20,7 +20,9 @@
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## * GHA: GitHub Action
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## * OS: operating system
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on: push
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on:
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push:
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pull_request:
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name: R-CMD-check-bioc
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@@ -50,9 +52,11 @@ jobs:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: 'release', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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- { os: macOS-latest, r: 'release', bioc: 'devel'}
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- { os: windows-latest, r: 'release', bioc: 'devel'}
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- { os: ubuntu-latest, r: '4.5', bioc: '3.22', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
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- { os: macOS-latest, r: '4.5', bioc: '3.22'}
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- { os: windows-latest, r: '4.5', bioc: '3.22'}
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## Check https://github.com/r-lib/actions/tree/master/examples
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## for examples using the http-user-agent
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
@@ -75,48 +79,49 @@ jobs:
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## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
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## If they update their steps, we will also need to update ours.
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- name: Checkout Repository
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uses: actions/checkout@v2
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uses: actions/checkout@v3
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## R is already included in the Bioconductor docker images
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- name: Setup R from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-r@master
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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## pandoc is already included in the Bioconductor docker images
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- name: Setup pandoc from r-lib
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if: runner.os != 'Linux'
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uses: r-lib/actions/setup-pandoc@master
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uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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- name: Cache R packages
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- name: Restore R package cache
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-
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- name: Cache R packages on Linux
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if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
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uses: actions/cache@v2
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uses: actions/cache@v3
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with:
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path: /home/runner/work/_temp/Library
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
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key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-
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- name: Install Linux system dependencies
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if: runner.os == 'Linux'
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run: |
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sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
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echo $sysreqs
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sudo -s eval "$sysreqs"
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# - name: Install Linux system dependencies
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# if: runner.os == 'Linux'
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# run: |
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# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
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# echo $sysreqs
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# sudo -s eval "$sysreqs"
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- name: Install macOS system dependencies
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if: matrix.config.os == 'macOS-latest'
@@ -135,6 +140,9 @@ jobs:
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## For installing usethis's dependency gert
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brew install libgit2
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## Required for tcltk
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brew install xquartz --cask
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- name: Install Windows system dependencies
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if: runner.os == 'Windows'
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run: |
@@ -149,7 +157,7 @@ jobs:
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- name: Set BiocVersion
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run: |
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
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BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
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shell: Rscript {0}
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- name: Install dependencies pass 1
@@ -161,9 +169,13 @@ jobs:
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## https://github.com/r-lib/remotes/issues/296
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## Ideally, all dependencies should get installed in the first pass.
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## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
174+
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
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## Pass #1 at installing dependencies
165177
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
166-
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
178+
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
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continue-on-error: true
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shell: Rscript {0}
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@@ -172,11 +184,6 @@ jobs:
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## Pass #2 at installing dependencies
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message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
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remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
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176-
## For running the checks
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message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
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remotes::install_cran("rcmdcheck")
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BiocManager::install("BiocCheck")
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shell: Rscript {0}
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- name: Install BiocGenerics
@@ -187,15 +194,15 @@ jobs:
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shell: Rscript {0}
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- name: Install covr
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if: github.ref == 'refs/heads/bioc-check' && env.run_covr == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
192199
remotes::install_cran("covr")
193200
shell: Rscript {0}
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195202
- name: Install pkgdown
196-
if: github.ref == 'refs/heads/bioc-check' && env.run_pkgdown == 'true' && runner.os == 'Linux'
203+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
197204
run: |
198-
remotes::install_cran("pkgdown")
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remotes::install_github("r-lib/pkgdown")
199206
shell: Rscript {0}
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201208
- name: Session info
@@ -208,10 +215,12 @@ jobs:
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- name: Run CMD check
209216
env:
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_R_CHECK_CRAN_INCOMING_: false
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DISPLAY: 99.0
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run: |
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options(crayon.enabled = TRUE)
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rcmdcheck::rcmdcheck(
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args = c("--no-build-vignettes", "--no-manual", "--timings"),
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build_args = c("--no-manual", "--no-resave-data"),
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args = c("--no-manual", "--no-vignettes", "--timings"),
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build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
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error_on = "warning",
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check_dir = "check"
217226
)
@@ -229,6 +238,8 @@ jobs:
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shell: Rscript {0}
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- name: Run BiocCheck
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env:
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DISPLAY: 99.0
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run: |
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BiocCheck::BiocCheck(
234245
dir('check', 'tar.gz$', full.names = TRUE),
@@ -239,40 +250,89 @@ jobs:
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shell: Rscript {0}
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241252
- name: Test coverage
242-
if: github.ref == 'refs/heads/bioc-check' && env.run_covr == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
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run: |
244-
covr::codecov()
255+
covr::codecov(coverage = covr::package_coverage(type = "all"))
245256
shell: Rscript {0}
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247258
- name: Install package
248-
if: github.ref == 'refs/heads/bioc-check' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: R CMD INSTALL .
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251-
- name: Deploy package
252-
if: github.ref == 'refs/heads/bioc-check' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
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git config --local user.email "[email protected]"
255-
git config --local user.name "GitHub Actions"
256-
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
257-
shell: bash {0}
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- name: Build pkgdown site
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
259267
## at least one locally before this will work. This creates the gh-pages
260268
## branch (erasing anything you haven't version controlled!) and
261269
## makes the git history recognizable by pkgdown.
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- name: Install deploy dependencies
272+
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
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run: |
274+
apt-get update && apt-get -y install rsync
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- name: Deploy pkgdown site to GitHub pages 🚀
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if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
278+
uses: JamesIves/github-pages-deploy-action@releases/v4
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with:
280+
clean: false
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branch: gh-pages
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folder: docs
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@v2
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uses: actions/upload-artifact@master
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with:
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name: ${{ runner.os }}-biocversion-devel-r-4.1-results
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name: ${{ runner.os }}-biocversion-devel-r-4.5-results
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path: check
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270-
- uses: docker/build-push-action@v1
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
291+
292+
## Code adapted from
293+
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
294+
docker-build-and-push:
295+
runs-on: ubuntu-latest
296+
needs: build-check
297+
steps:
298+
- name: Checkout Repository
299+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
300+
uses: actions/checkout@v3
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302+
- name: Register repo name
303+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
304+
id: reg_repo_name
305+
run: |
306+
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
307+
308+
- name: Set up QEMU
309+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
310+
uses: docker/setup-qemu-action@v2
311+
312+
- name: Set up Docker Buildx
313+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/setup-buildx-action@v2
315+
316+
- name: Login to Docker Hub
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if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
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uses: docker/login-action@v2
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with:
320+
username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
322+
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
323+
## account, not your actual dockerhub account password. You can get it
324+
## from https://hub.docker.com/settings/security.
325+
## Check https://github.com/docker/build-push-action/tree/v4.0.0
326+
## for more details.
327+
## Alternatively, try checking
328+
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
329+
330+
- name: Build and Push Docker
331+
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
332+
uses: docker/build-push-action@v4
272333
with:
273-
username: ${{ secrets.DOCKER_USERNAME }}
274-
password: ${{ secrets.DOCKER_PASSWORD }}
275-
repository: mfansler/txcutr
276-
tag_with_ref: true
277-
tag_with_sha: true
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tags: latest
334+
context: .
335+
push: true
336+
tags: >
337+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
338+
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

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